|
| Status |
Public on Jul 01, 2020 |
| Title |
A549 cells, 2D-cultured, control-treated |
| Sample type |
RNA |
| |
|
| Source name |
A549 cells, 2D-cultured, control-treated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
activating egfr mutation: no
treatment: control
cell culture: 2D
|
| Treatment protocol |
Control samples were cultured without inhibitor treatment as described above for both culture conditions. The EGFR-Inhibitor gefitinib was applied after 11 days of static culture at a concentration of 1µM for the following 3 days under 3D culture conditions. Under 3D conditions gefitinib was applied after 4 days of culture at a concentration of 1µM.
|
| Growth protocol |
For 3D conditions, 100.000 cells per cell line were seeded onto a collagen scaffold and cultured for 14 days under static conditions at 37°C with 5% CO2 and 95% humidity. Under 2D conditions, 200.000 cells were seeded onto 21cm² culture dishes and cultured for 7 days at 37°C with 5% CO2 and 95% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Collagen matrices with cells were harvested and frozen at -80°C. Frozen samples were cut into small pieces and lysed using metal beads and the Qiagen TissueLyser at 50Hz for 5min. RNA extraction was carried out according to the Qiagen RNeasy micro kit (3D samples) or RNeasy mini kit (2D samples) protocols.
|
| Label |
biotin
|
| Label protocol |
100ng of total RNA were amplified and labeled with the IVT PLUS Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.
|
| |
|
| Hybridization protocol |
130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.
|
| Scan protocol |
Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).
|
| Data processing |
Data were preprocessed in the R v3.2.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.
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| |
|
| Submission date |
Mar 10, 2016 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Claus Juergen Scholz |
| Organization name |
University Hospital Würzburg
|
| Department |
Core Unit SysMed
|
| Street address |
Josef-Schneider-Str. 2
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16043 |
| Series (1) |
| GSE79078 |
Gene expression after treatment in a 3D lung tumor model in comparison to conventional 2D cell culture |
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